Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

Complete genome sequence analysis and identification of putative metallo-beta-lactamase and SpoIIIE homologs in Bacillus cereus group phage BCP8-2, a new member of the proposed Bastille-like group

(2015) Paul Tetteh Asare et al.   ARCHIVES OF VIROLOGY

Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel bastille-like group of phages in the subfamily Spounavirinae

(2015) Paul Tetteh Asare et al.   BMC GENOMICS

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Current perspectives on the dynamics of antibiotic resistance in different reservoirs

(2015) Manuela Caniça et al.   RESEARCH IN MICROBIOLOGY

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Comparative Genomics of Cluster O Mycobacteriophages

(2015) Steven G. Cresawn et al.   PLoS One

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes

(2015) Shira R. Abeles et al.   PLoS One

The Novel Macrolide-Lincosamide-Streptogramin B Resistance Geneerm(44) Is Associated with a Prophage in Staphylococcus xylosus

(2014) Juliette R. K. Wipf et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of a P1-Like Bacteriophage Carrying an SHV-2 Extended-Spectrum β-Lactamase from an Escherichia coli Strain

(2014) Typhaine Billard-Pomares et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread

(2014) Victoriya V. Volkova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment

(2014) Jose Luis Balcazar   PLoS Pathogens

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Nucleotide sequence of conjugative prophage Φ1207.3 (formerly Tn1207.3) carrying the mef(A)/msr(D) genes for efflux resistance to macrolides in Streptococcus pyogenes

(2014) Francesco Iannelli et al.   Frontiers in Microbiology

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

(2014) Jennifer R Huddleston   Infection and Drug Resistance

Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Human Fecal Samples

(2013) Pablo Quirós et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

(2013) Aimée M. Moore et al.   PLoS One

Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

(2013) Lesley A. Ogilvie et al.   Nature Communications

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

(2013) S. Roux et al.   Open Biology

The human microbiome as a reservoir of antimicrobial resistance

(2013) John Penders et al.   Frontiers in Microbiology

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Hypervariable loci in the human gut virome

(2012) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples

(2011) Gloria Torres-Cortés et al.   ENVIRONMENTAL MICROBIOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Bacteriophages as vehicles of the resistome in cystic fibrosis

(2011) J. M. Rolain et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota

(2011) L. Fancello et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis

(2011) Maria M. Klimecka et al.   JOURNAL OF MOLECULAR BIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes

(2011) H. K. Allen et al.   mBio

Identification of Diverse Antimicrobial Resistance Determinants Carried on Bacterial, Plasmid, or Viral Metagenomes from an Activated Sludge Microbial Assemblage

(2010) L. C. Parsley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

The phage-related chromosomal islands of Gram-positive bacteria

(2010) Richard P. Novick et al.   NATURE REVIEWS MICROBIOLOGY

 m46.1, the Main Streptococcus pyogenes Element Carrying mef(A) and tet(O) Genes

(2009) A. Brenciani et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Tetracycline Resistome of the Organic Pig Gut

(2009) K. A. Kazimierczak et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Metagenomic Screening for Bleomycin Resistance Genes

(2008) T. Mori et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil

(2008) Heather K Allen et al.   ISME Journal

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH